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Protein

Acyl-CoA thioesterase YbgC

Gene

ybgC

Organism
Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Thioesterase that may be involved in phospholipid metabolism. Displays acyl-CoA thioesterase activity with lauroyl-CoA (C12:0), myristoyl-CoA (C14:0), palmitoyl-CoA (C16:0), stearoyl-CoA (C18:0) and benzoyl-CoA, catalyzing the hydrolysis of the thioester bond. Has low activity with butyryl-CoA and octanoyl-CoA.1 Publication

Kineticsi

kcat is 0.028 sec(-1) with benzoyl-CoA, 0.034 sec(-1) with stearoyl-CoA, 0.045 sec(-1) with palmitoyl-CoA, 0.024 sec(-1) with myristoyl-CoA, 0.015 sec(-1) with lauroyl-CoA and 0.0013 sec(-1) with octanoyl-CoA.

  1. KM=200 µM for benzoyl-CoA
  2. KM=210 µM for stearoyl-CoA
  3. KM=570 µM for palmitoyl-CoA
  4. KM=240 µM for myristoyl-CoA
  5. KM=160 µM for lauroyl-CoA
  6. KM=40 µM for octanoyl-CoA
  7. KM=27 µM for butyryl-CoA

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Active sitei11PROSITE-ProRule annotation1

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Lipid metabolism

    Enzyme and pathway databases

    BioCyciHPY:HP0496-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Acyl-CoA thioesterase YbgC (EC:3.1.2.-)
    Gene namesi
    Name:ybgC
    Ordered Locus Names:HP_0496
    OrganismiHelicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
    Taxonomic identifieri85962 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaEpsilonproteobacteriaCampylobacteralesHelicobacteraceaeHelicobacter
    Proteomesi
    • UP000000429 Componenti: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00000877671 – 133Acyl-CoA thioesterase YbgCAdd BLAST133

    Proteomic databases

    PaxDbiP94842.

    Interactioni

    Subunit structurei

    Homotetramer. May interact with CagA.1 Publication

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    cagAP559802EBI-528090,EBI-528104

    Protein-protein interaction databases

    DIPiDIP-3437N.
    IntActiP94842. 1 interactor.
    MINTiMINT-167425.
    STRINGi85962.HP0496.

    Structurei

    Secondary structure

    1133
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi1 – 4Combined sources4
    Helixi7 – 9Combined sources3
    Beta strandi14 – 16Combined sources3
    Helixi20 – 34Combined sources15
    Turni35 – 37Combined sources3
    Beta strandi40 – 42Combined sources3
    Beta strandi45 – 56Combined sources12
    Beta strandi65 – 75Combined sources11
    Beta strandi77 – 90Combined sources14
    Beta strandi100 – 112Combined sources13
    Turni114 – 116Combined sources3
    Helixi124 – 131Combined sources8

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2PZHX-ray1.70A/B/C/D1-133[»]
    ProteinModelPortaliP94842.
    SMRiP94842.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP94842.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4107YD3. Bacteria.
    COG0824. LUCA.
    KOiK07107.
    OMAiFPIRVYW.

    Family and domain databases

    Gene3Di3.10.129.10. 1 hit.
    InterProiIPR008272. HB-CoA_thioesterase_AS.
    IPR029069. HotDog_dom.
    IPR006683. Thioestr_dom.
    IPR006684. YbgC/YbaW.
    [Graphical view]
    PfamiPF03061. 4HBT. 1 hit.
    [Graphical view]
    PIRSFiPIRSF003230. YbgC. 1 hit.
    SUPFAMiSSF54637. SSF54637. 1 hit.
    TIGRFAMsiTIGR00051. TIGR00051. 1 hit.
    PROSITEiPS01328. 4HBCOA_THIOESTERASE. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P94842-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MRCRVYYEDT DSEGVVYHAN YLKYCERARS EFFFKQNVLP ENEEGVFVIR
    60 70 80 90 100
    SIKADFFTPA SLGQVLEIRT QIKELRKVFV VLFQEIYCIQ NASLEPMKPF
    110 120 130
    KVFASEIKFG FVNRSTYSPI AIPKLFKELL NAI
    Length:133
    Mass (Da):15,596
    Last modified:July 15, 1999 - v2
    Checksum:i18C969BB96B802F9
    GO

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti133I → V in AAB39716 (Ref. 1) Curated1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U75328 Genomic DNA. Translation: AAB39716.1.
    AE000511 Genomic DNA. Translation: AAD07561.1.
    PIRiH64581.
    RefSeqiNP_207293.1. NC_000915.1.
    WP_001203797.1. NC_018939.1.

    Genome annotation databases

    EnsemblBacteriaiAAD07561; AAD07561; HP_0496.
    GeneIDi900055.
    KEGGiheo:C694_02550.
    hpy:HP0496.
    PATRICi20592267. VBIHelPyl33062_0522.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U75328 Genomic DNA. Translation: AAB39716.1.
    AE000511 Genomic DNA. Translation: AAD07561.1.
    PIRiH64581.
    RefSeqiNP_207293.1. NC_000915.1.
    WP_001203797.1. NC_018939.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2PZHX-ray1.70A/B/C/D1-133[»]
    ProteinModelPortaliP94842.
    SMRiP94842.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    DIPiDIP-3437N.
    IntActiP94842. 1 interactor.
    MINTiMINT-167425.
    STRINGi85962.HP0496.

    Proteomic databases

    PaxDbiP94842.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAD07561; AAD07561; HP_0496.
    GeneIDi900055.
    KEGGiheo:C694_02550.
    hpy:HP0496.
    PATRICi20592267. VBIHelPyl33062_0522.

    Phylogenomic databases

    eggNOGiENOG4107YD3. Bacteria.
    COG0824. LUCA.
    KOiK07107.
    OMAiFPIRVYW.

    Enzyme and pathway databases

    BioCyciHPY:HP0496-MONOMER.

    Miscellaneous databases

    EvolutionaryTraceiP94842.

    Family and domain databases

    Gene3Di3.10.129.10. 1 hit.
    InterProiIPR008272. HB-CoA_thioesterase_AS.
    IPR029069. HotDog_dom.
    IPR006683. Thioestr_dom.
    IPR006684. YbgC/YbaW.
    [Graphical view]
    PfamiPF03061. 4HBT. 1 hit.
    [Graphical view]
    PIRSFiPIRSF003230. YbgC. 1 hit.
    SUPFAMiSSF54637. SSF54637. 1 hit.
    TIGRFAMsiTIGR00051. TIGR00051. 1 hit.
    PROSITEiPS01328. 4HBCOA_THIOESTERASE. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiYBGC_HELPY
    AccessioniPrimary (citable) accession number: P94842
    Secondary accession number(s): O25238
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 15, 1999
    Last sequence update: July 15, 1999
    Last modified: November 2, 2016
    This is version 108 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Helicobacter pylori
      Helicobacter pylori (strain 26695): entries and gene names
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.